My Magento version is 126.96.36.199 and had SUPEE-1533 installed.
As per Magento guidelines I have reverted this patch and then applied SUPEE-3941 (previously not applied). These step went successfully. Now when I tried to apply
PATCH_SUPEE-8788_EE_188.8.131.52_v2-2016-10-14-11-52-21.sh throwing below error output -
$ ./PATCH_SUPEE-8788_EE_184.108.40.206_v2-2016-10-14-11-52-21.sh` Checking if patch can be applied/reverted successfully... /usr/bin/patch: malformed patch at line 6139: ERROR: Patch can't be applied/reverted successfully.
I have downloaded patch file directly from Magento server.